unanswered scfix flag does not work for Martini22 force field

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2 years 9 months ago #9192 by azadehalavi
Dear all,

I would like to use martinize2 program to create a coarse-grain model of my membrane-peptide system.

It seems that the -scfix flag does not work for Martini 2 (for Martini 3 it works), I added -scfix flag to the martinize2 command and I got this warning:

WARNING - missing-feature - The force field "martini22" does not define angle and torsion for the side chain corrections (-scfix)

So does this mean that the bbsc.sh script should be used?

Also, are the side-chain corrections necessary for single alpha helix transmembrane proteins?

I would appreciate your help.

Best regards,
Azadeh

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